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At least 55 records · Page 3

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.

Drago, Victoria N. [Oak Ridge National Laboratory ↗

Search for $t\bar{t}H/A$ → $t\bar{t}t\bar{t}$ production in the multilepton final state in proton–proton collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

A search for a new heavy scalar or pseudo-scalar Higgs boson ($H/A$) produced in association with a pair of top quarks, with the Higgs boson decaying into a pair of top quarks ($H/A$ → $t\bar{t}$) is reported. The search targets a final state with exactly two leptons with same-sign electric charges or at least three leptons. The analysed dataset corresponds to an integrated luminosity of 139 fb –1 of proton–proton collisions collected at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC. Two multivariate classifiers are used to separate the signal from the background. No significant excess of events over the Standard Model expectation is observed. The results are interpreted in the context of a type-II two-Higgs-doublet model. The observed (expected) upper limits at 95% confidence level on the $t\bar{t}$$H/A$ production cross-section times the branching ratio of $H/A$ → $t\bar{t}$ range between 14 (10) fb and 6 (5) fb for a heavy Higgs boson with mass between 400 GeV and 1000 GeV, respectively. Assuming that only one particle, either the scalar $H$ or the pseudo-scalar $A$, contributes to the $t\bar{t}t\bar{t}$ final state, values of tan $β$ below 1.2 or 0.5 are excluded for a mass of 400 GeV or 1000 GeV, respectively. These exclusion ranges increase to tan $β$ below 1.6 or 0.6 when both particles are considered.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurement of $t\overline{t}$ production in association with additional b -jets in the eμ final state in proton–proton collisions at $\sqrt{s}$ = 13 TeV with the ATLAS detector

This paper presents measurements of top-antitop quark pair ($t\overline{t}$) production in association with additional b-jets. The analysis utilises 140 fb -1 of proton–proton collision data collected with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 13 TeV. Fiducial cross-sections are extracted in a final state featuring one electron and one muon, with at least three or four b-jets. Results are presented at the particle level for both integrated cross-sections and normalised differential cross-sections, as functions of global event properties, jet kinematics, and b-jet pair properties. Observable quantities characterising b-jets originating from the top quark decay and additional b-jets are also measured at the particle level, after correcting for detector effects. The measured integrated fiducial cross sections are consistent with $t\overline{t}$$b\overline{b}$ predictions from various next-to-leading-order matrix element calculations matched to a parton shower within the uncertainties of the predictions. State of-the-art theoretical predictions are compared with the differential measurements; none of them simultaneously describes all observables. Differences between any two predictions are smaller than the measurement uncertainties for most observables.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Differential charge radii: Proton-neutron interaction effects

The analysis of self-consistency and proton-neutron interaction effects in the buildup of differential charge radii were carried out in covariant density functional theoretical calculations without pairing interaction on the example of selected configurations in the Pb isotopes. The proton-neutron interaction of neutron(s) added to the neutron 𝑁 = 126 core and the protons forming the 𝑍 = 82 proton core is responsible for a major contribution to the buildup of differential charge radii. It depends on the products of proton and neutron wave functions and thus on their nodal structure. This interaction leads to a redistribution of single-particle density of occupied proton states which in turn modifies the charge radii. Furthermore, the microscopic origin of this redistribution and its consequences for differential charge radii were investigated for the first time. Self-consistency effects affecting the shape of proton potential, total proton densities and the energies of the single-particle proton states provide only minor contribution to differential charge radii.

190 ≤ A ≤ 219↗

The diffractive contribution to deep inelastic lepton-proton scattering: Implications for QCD momentum sum rules and parton distributions

The cross section for deep inelastic lepton-proton scattering (DIS) ℓp→ℓ'p'X includes a diffractive deep inelastic (DDIS) contribution ℓp→ℓ'p'X, in which the proton remains intact with a large longitudinal momentum fraction x F greater than 0.9 and small transverse momentum. The DDIS events, which can be identified with Pomeron exchange in the t-channel, account for approximately 10% of all of the DIS events. Thus, when one measures DIS, one automatically includes the leading-twist Bjorken-scaling DDIS events as a contribution to the DIS cross section, whether or not the final-state proton p' is detected. In such events, the missing momentum fraction x p ' ~0.9 carried by the final-state proton p' in the DDIS events could be misidentified with the light-front momentum fraction carried by sea quarks or gluons in the protons' Fock structure. As we shall show in this article, the underlying QCD Pomeron-exchange amplitude which produces the DDIS events does not obey the operator product expansion nor satisfy momentum sum rules. Thus we conclude that the quark and gluon distributions measured in DIS experiments will be misidentified, unless the measurements explicitly exclude the DDIS events and that a correct determination of the parton distribution functions (PDFs) derived from the DIS data requires the explicit subtraction of the DDIS contribution from the full DIS cross section.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atomistic characterization of hydration-dependent fuel cell ionomer nanostructure: validation by vibrational spectroscopy

The development of Nafion alternatives for fuel cells and electrolyzers requires a fundamental understanding of hydration-dependent ion-exchange site acid/base chemistry. We present here reactive force field (ReaxFF) molecular dynamics (MD) simulations of Nafion at varying molar water/ion-exchange-site ratios (λ), which we correlate to our experimental and density functional theory-based vibrational spectra. ReaxFF describes the formation and breaking of covalent bonds, enabling simulations of proton exchange between sulfonic acid/sulfonate groups and water/hydronium. Our MD simulations determine the λ-dependent equilibrium proportions of protonated and deprotonated sites. We find that protonated sites persist across all λ from 0 to 20, challenging the widely accepted notion that all sites are ionized above a threshold λ value (e.g., 3 or 4). Our simulations generate hundreds of realistic exchange site environments, the characterization of which are based on 6 Å radii sulfur-centered ‘inner-spheres’. These inner- and outer-sphere regions elucidate an interplay of stereoelectronic factors that influence protonation states, including the number of inner-sphere waters (Λ). Our simulations produce broad λ-dependent distributions of Λ values, representing non-uniform exchange site hydration. Moreover, we demonstrate that these distributions are specific to both protonated and deprotonated sites, with significant overlap between the two distributions for all non-zero λ. These distributions underpin the IR spectra of hydrated membranes, with each exchange site contributing an IR spectrum characteristic of its protonation state and Λ. We expect that these nanostructural characterizations of Nafion exchange sites will contribute to the development of new ionomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Search for heavy resonances decaying into two Higgs bosons in the $\text {b}{\bar{\text {b}}} \tau ^{+} \tau ^{-}$ final state in proton–proton collisions at $\sqrt{s} = 13\,\text {Te}\hspace{-.08em}\text {V}$

A search is presented for massive narrow-width resonances in the mass range of 1–4.5 TeV , decaying into pairs of Higgs bosons (HH). The search uses proton–proton collision data at a center-of-mass energy of 13 TeV collected with the CMS detector at the CERN LHC during 2016–2018, corresponding to an integrated luminosity of 138 fb -1 . The analysis targets final states where one Higgs boson decays into a pair of bottom quarks and the other into a pair of tau leptons, ${\text {X}} \rightarrow {\text {HH}} \rightarrow \text {b}{\bar{\text {b}}}\,\tau ^{+}\tau ^{-}$. It uses a single large radius jet to reconstruct the ${\text {H}} \rightarrow \text {b}{\bar{\text {b}}}$ decay, while the ${\text {H}} \rightarrow \tau ^{+}\tau ^{-}$ decay products can either be contained within a single large radius jet or appear as two isolated tau leptons. The observed data are consistent with standard model background expectations. Upper limits at 95% confidence level are set on the production cross section for resonant HH production for masses between 1 and 4.5 TeV. This analysis sets the most sensitive limits to date on ${\text {X}} \rightarrow {\text {HH}} \rightarrow \text {b}\bar{\hbox {b}}\, \tau ^{+}\tau ^{-}$ decays in the mass range of 1.4–4.5 TeV.

Hayrapetyan, A. [Yerevan Physics Institute]↗

Measurement of the top quark mass using a profile likelihood approach with the lepton + jets final states in proton–proton collisions at $\sqrt{s}=13\,\text {Te}\hspace{-.08em}\text {V}$

The mass of the top quark is measured in 36.3 fb -1 of LHC proton–proton collision data collected with the CMS detector at $\sqrt{s}=13\,\text {Te}\hspace{-.08em}\text {V}$. The measurement uses a sample of top quark pair candidate events containing one isolated electron or muon and at least four jets in the final state. For each event, the mass is reconstructed from a kinematic fit of the decay products to a top quark pair hypothesis. A profile likelihood method is applied using up to four observables per event to extract the top quark mass. The top quark mass is measured to be 171.77 ± 0.37 GeV. This approach significantly improves the precision over previous measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions

Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper–oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallo­graphy provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. Here, to characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

Neurospora crassa↗

Enhanced search for neutral current Δ radiative single-photon production in MicroBooNE

We report results from an updated search for neutral current (NC) resonant Δ⁡(1232) baryon production and subsequent Δ radiative decay (NC Δ → 𝑁⁢𝛾). We consider events with and without final state protons; events with a proton can be compared with the kinematics of a Δ⁡(1232) baryon decay, while events without a visible proton represent a more generic phase space. In order to maximize sensitivity to each topology, we simultaneously make use of two different reconstruction paradigms, Pandora and Wire-Cell, which have complementary strengths, and select mostly orthogonal sets of events. Considering an overall scaling of the NC Δ → 𝑁⁢𝛾 rate as an explanation of the MiniBooNE anomaly, our data exclude this hypothesis at 94.4% CL. When we decouple the expected correlations between NC Δ → 𝑁⁢𝛾 events with and without final state protons, our data exclude an interpretation in which all excess events have associated protons at 2.0⁢𝜎, and are consistent with an interpretation in which all excess events have no associated protons at 0.63⁢𝜎.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The solution structures and relative stability constants of lanthanide–EDTA complexes predicted from computation

Ligand selectivity to specific lanthanide (Ln) ions is key to the separation of rare earth elements from each other. Ligand selectivity can be quantified with relative stability constants (measured experimentally) or relative binding energies (calculated computationally). The relative stability constants of EDTA (ethylenediaminetetraacetic acid) with La 3+ , Eu 3+ , Gd 3+ , and Lu 3+ were predicted from relative binding energies, which were quantified using electronic structure calculations with relativistic effects and based on the molecular structures of Ln–EDTA complexes in solution from density functional theory molecular dynamics simulations. The protonation state of an EDTA amine group was varied to study pH ~7 and ~11 conditions. Further, simulations at 25 °C and 90 °C were performed to elucidate how structures of Ln–EDTA complexes varying with temperature are related to complex stabilities at different pH conditions. Relative stability trends are predicted from computation for varying Ln 3+ ions (La, Eu, Gd, Lu) with a single ligand (EDTA at pH ~11), as well as for a single Ln 3+ ion (La) with varying ligands (EDTA at pH ~7 and ~11). Changing the protonation state of an EDTA amine site significantly changes the solution structure of the Ln–EDTA complex resulting in a reduction of the complex stability. As a result, increased Ln–ligand complex stability is correlated to reduced structural variations in solution upon an increase in temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure

Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.

4K-TMA↗

Search for pair production of heavy particles decaying to a top quark and a gluon in the lepton+jets final state in proton–proton collisions at $\sqrt{s}=13\,\text {Te}\hspace{-.08em}\text {V}$

A search is presented for the pair production of new heavy resonances, each decaying into a top quark (t) or antiquark and a gluon (g). The analysis uses data recorded with the CMS detector from proton–proton collisions at a center-of-mass energy of 13 TeV at the LHC, corresponding to an integrated luminosity of 138 fb -1 . Events with one muon or electron, multiple jets, and missing transverse momentum are selected. After using a deep neural network to enrich the data sample with signal-like events, distributions in the scalar sum of the transverse momenta of all reconstructed objects are analyzed in the search for a signal. No significant deviations from the standard model prediction are found. Upper limits at 95% confidence level are set on the product of cross section and branching fraction squared for the pair production of excited top quarks in the t* → tg decay channel. The upper limits range from 120 to 0.8 fb for a t* with spin-1/2 and from 15 to 1.0 fb for a t* with spin-3/2. These correspond to mass exclusion limits up to 1050 and 1700 GeV for spin-1/2 and spin-3/2 t* particles, respectively. These are the most stringent limits to date on the existence of t* → tg resonances.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Highly Altered State of Proton Transport in Acid Pools in Charged Reverse Micelles

Transport mechanisms of solvated protons of 1 M HCl acid pools, confined within reverse micelles (RMs) containing the negatively charged surfactant sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) or the positively charged cetyltrimethylammonium bromide (CTABr), are analyzed with reactive force field simulations to interpret dynamical signatures from TeraHertz absorption and dielectric relaxation spectroscopy. We find that the forward proton hopping events for NaAOT are further suppressed compared to a nonionic RM, while the Grotthuss mechanism ceases altogether for CTABr. We attribute the sluggish proton dynamics for both charged RMs as due to headgroup and counterion charges that expel hydronium and chloride ions from the interface and into the bulk interior, thereby increasing the pH of the acid pools relative to the nonionic RM. For charged NaAOT and CTABr RMs, the localization of hydronium near a counterion or conjugate base reduces the Eigen and Zundel configurations that enable forward hopping. Thus, localized oscillatory hopping dominates, an effect that is most extreme for CTABr in which the proton residence time increases dramatically such that even oscillatory hopping is slow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evidence for $t\bar{t}t\bar{t}$ production in the multilepton final state in proton–proton collisions at $\sqrt{s}=13$ $\text {TeV}$ with the ATLAS detector

A search is presented for four-top-quark production using an integrated luminosity of 139 fb –1 of proton–proton collision data at a centre-of-mass energy of 13 TeV collected by the ATLAS detector at the LHC. Events are selected if they contain a same-sign lepton pair or at least three leptons (electrons or muons). Jet multiplicity, jet flavour and event kinematics are used to separate signal from the background through a multivariate discriminant, and dedicated control regions are used to constrain the dominant backgrounds. The four-top-quark production cross section is measured to be $24^{+7}_{–6}$ fb. This corresponds to an observed (expected) significance with respect to the background-only hypothesis of 4.3 (2.4) standard deviations and provides evidence for this process.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurements of production cross sections of the Higgs boson in the four-lepton final state in proton–proton collisions at $\sqrt{s} = 13\,\text {Te}\text {V} $

Production cross sections of the Higgs boson are measured in the H $\to$ ZZ $\to$ $4\ell$ ($\ell$ $=$ e, $\mu$) decay channel. A data sample of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the CMS detector at the LHC and corresponding to an integrated luminosity of 137 fb$^{-1}$ is used. The signal strength modifier $\mu$, defined as the ratio of the Higgs boson production rate in the $4\ell$ channel to the standard model (SM) expectation, is measured to be $\mu$ $=$ 0.94 $\pm$ 0.07 (stat) ${}^{+0.09}_{-0.08}$ (syst) at a fixed value of $m_H$ = 125.38 GeV. The signal strength modifiers for the individual Higgs boson production modes are also reported. The inclusive fiducial cross section for the H $\to$ $4\ell$ process is measured to be 2.84 $^{+0.23}_{-0.22}$ (stat) ${}^{+0.26}_{-0.21}$ (syst) fb, which is compatible with the SM prediction of 2.84 $\pm$ 0.15 fb for the same fiducial region. Differential cross sections as a function of the transverse momentum and rapidity of the Higgs boson, the number of associated jets, and the transverse momentum of the leading associated jet are measured. A new set of cross section measurements in mutually exclusive categories targeted to identify production mechanisms and kinematical features of the events is presented. The results are in agreement with the SM predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Boundary of the Distribution of Solar Wind Proton Beta versus Temperature Anisotropy

Abstract The frequency distribution of solar wind protons, measured in the vicinity of Earth’s orbit, is customarily plotted in ( β ∥ , T ⊥ / T ∥ ) phase space. Here, T ⊥ / T ∥ is the ratio of perpendicular and parallel temperatures, and β ∥ = 8 π nT ∥ / B 2 is the ratio of parallel thermal energy to background magnetic field energy, the so-called “parallel beta,” with ⊥ and ∥ denoting directions with respect to the ambient magnetic field. Such a frequency distribution, plotted as a two-dimensional histogram, forms a peculiar rhombic shape defined with an outer boundary in the said phase space. Past studies reveal that the threshold conditions for temperature anisotropy–driven plasma instability partially account for the boundary on the high- β ∥ side. The low- β ∥ side remains largely unexplained despite some efforts. Work by Vafin et al. recently showed that certain contours of collisional relaxation frequency, ν pp , when parameterized by T ⊥ / T ∥ and β ∥ , could match the overall shape of the left-hand boundary, thus suggesting that the collisional relaxation process might be closely related to the formation of the left-hand boundary. The present paper extends the analysis by Vafin et al. and carries out the dynamical computation of the collisional relaxation process for an ensemble of initial proton states with varying degrees of anisotropic temperatures. The final states of the relaxed protons are shown to closely match the observed boundary to the left of the ( β ∥ , T ⊥ / T ∥ ) phase space. When coupled with a similar set of calculations for the ensemble in the collective instability regime, it is found that the combined collisional/collective effects provide the baseline explanation for the observation.

Astronomy & Astrophysics↗

Proton Dissociation and Delocalization under Stepwise Hydration of Zeolite HZSM-5

The protonation behavior of zeolite Brønsted acid sites (BAS) in the presence of water is important for the performance of these widely used catalysts. Despite extensive study, the number of water molecules necessary for deprotonation is not well understood, in large part because experiments have been unable to access this information. In this work, we report experimental evidence for full deprotonation of the BAS in the presence of two or more water molecules, with a deprotonation energy of 1.6 kcal/mol. Linear IR absorption and 2D IR spectra were measured over a wide range of controlled hydration levels from 0.5 to 8.0 equivalents of H 2 O/Al at a constant temperature. Distinct spectral signatures of the protonated BAS and excess proton are identified, and their hydration dependence is analyzed quantitatively. Using the experiment as a benchmark, ab initio molecular dynamics simulations are reported that reproduce the experimental trends in the protonation state and IR spectra. The proton charge position and delocalization are quantified in clusters of 1–8 H 2 O molecules using the recently developed rCEC method. This analysis provides insight into the proton structure in confined water clusters, showing that the excess charge remains relatively localized between two oxygen atoms across the hydration range.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗